In [2]:
import sys 
import modeller 
import _modeller
import modeller.automodel 
from IPython.display import Image
In [3]:
#Зададим параметры
env=modeller.environ()
env.io.hetatm=True
                         MODELLER 9.24, 2020/04/06, r11614

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


                     Copyright(c) 1989-2020 Andrej Sali
                            All Rights Reserved

                             Written by A. Sali
                               with help from
              B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
          M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
             A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
                     F. Melo, J.P. Overington, E. Feyfant
                 University of California, San Francisco, USA
                    Rockefeller University, New York, USA
                      Harvard University, Cambridge, USA
                   Imperial Cancer Research Fund, London, UK
              Birkbeck College, University of London, London, UK


Kind, OS, HostName, Kernel, Processor: 4, Linux kodomo 3.16.0-6-amd64 x86_64
Date and time of compilation         : 2020/04/06 19:06:24
MODELLER executable type             : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2020/05/21 18:10:48

In [3]:
#Скачаем белок заготовку   P50718
! wget http://www.pdb.org/pdb/files/1lmp.pdb
--2020-05-21 16:54:47--  http://www.pdb.org/pdb/files/1lmp.pdb
Resolving www.pdb.org (www.pdb.org)... 128.6.244.52
Connecting to www.pdb.org (www.pdb.org)|128.6.244.52|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://www.rcsb.org/pdb/files/1lmp.pdb [following]
--2020-05-21 16:54:47--  https://www.rcsb.org/pdb/files/1lmp.pdb
Resolving www.rcsb.org (www.rcsb.org)... 128.6.244.65
Connecting to www.rcsb.org (www.rcsb.org)|128.6.244.65|:443... connected.
ERROR: The certificate of `www.rcsb.org' is not trusted.
ERROR: The certificate of `www.rcsb.org' hasn't got a known issuer.
In [23]:
#Скачаем последовательность лизоцима мотылька
! wget http://www.uniprot.org/uniprot/P50718.fasta
--2020-05-21 17:57:56--  http://www.uniprot.org/uniprot/Q7SID7.fasta
Resolving www.uniprot.org (www.uniprot.org)... 128.175.245.202, 193.62.192.81
Connecting to www.uniprot.org (www.uniprot.org)|128.175.245.202|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://www.uniprot.org:443/uniprot/Q7SID7.fasta [following]
--2020-05-21 17:57:57--  https://www.uniprot.org/uniprot/Q7SID7.fasta
Connecting to www.uniprot.org (www.uniprot.org)|128.175.245.202|:443... connected.
HTTP request sent, awaiting response... 200 
Length: 192 [text/plain]
Saving to: `Q7SID7.fasta'

100%[======================================>] 192         --.-K/s   in 0s      

2020-05-21 17:57:58 (84.5 MB/s) - `Q7SID7.fasta' saved [192/192]

In [13]:
#Создадим объект выравнивание 
alignm=modeller.alignment(env)
In [14]:
alignm.append(file='P50718.fasta', align_codes='all',alignment_format='FASTA')
## создадим модель
mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
## и добавим в выравнивание
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')
## есть смысл поправить идентификаторы
alignm[0].code = 'LYS_TRINI' 
alignm[1].code = '1lmp'
In [15]:
#Делаем выравнивание и сохраняем
alignm.salign()
alignm.write(file='all_in_one.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration    1
In [16]:
! cat all_in_one.ali
>P1;LYS_TRINI
sequence::     : :     : :::-1.00:-1.00
MQKLRVFLLALAALCISCEAKYFATNCELVHELRRQGFPEDKMRDWVCLIQNESGRNTSKMGTINKNGSRDYGLF
QINDKYWCSKTSTPGKD--CNVTCAEMLLDDITKASKCAKKI-YKRHKFQAWYGWRNHCQGTLPDISKC------
-*

>P1;1lmp
structureX:1lmp.pdb:   1 :A:+132 :A:MOL_ID  1; MOLECULE  LYSOZYME; CHAIN  A; SYNONYM  MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC  3.2.1.17:MOL_ID  1; ORGANISM_SCIENTIFIC  ONCORHYNCHUS MYKISS; ORGANISM_COMMON  RAINBOW TROUT; ORGANISM_TAXID  8022; ORGAN  KIDNEY: 2.00: 0.16
KVYDRCELA------------------RALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNR-NTDGSTDYGIF
QINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV..
.*
С выравнивамнием кажется все ок
In [17]:
# Выбираем объект для моделирования.
s = alignm[0]
pdb = alignm[1]

print(s.code, pdb.code)

# Создаем объект automodel.
a = modeller.automodel.automodel(env, alnfile='all_in_one.ali', knowns=pdb.code, sequence=s.code)

a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
LYS_TRINI 1lmp
automodel__W> Topology and/or parameter libraries already in memory. These will
                be used instead of the automodel defaults. If this is not what you
                want, clear them before creating the automodel object with
                env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)

check_ali___> Checking the sequence-structure alignment. 

Implied intrachain target CA(i)-CA(i+1) distances longer than  8.0 angstroms:

ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
----------------------------------------------
     92     1   73    76      D     C    8.895
END OF TABLE
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL:        3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
              Default CHARMM atom type assigned:  C1 -->  CT2
              This message is written only for the first such atom.
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:    11787    10783
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      141
Number of all, selected real atoms                :     1135    1135
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    10783   10783
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2431
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        1088.7938





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    1158       0      1   0.008   0.008      18.820       1.000
 2 Bond angle potential               :    1555       1     12   2.360   2.360      171.60       1.000
 3 Stereochemical cosine torsion poten:     730       0     31  47.208  47.208      261.01       1.000
 4 Stereochemical improper torsion pot:     471       0      0   1.449   1.449      20.379       1.000
 5 Soft-sphere overlap restraints     :    2431       0      0   0.003   0.003      2.4318       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    2217       0      1   0.402   0.402      119.41       1.000
10 Distance restraints 2 (N-O)        :    2375       0      5   0.438   0.438      148.40       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     140       1      3   5.382   5.382      47.829       1.000
14 Sidechain Chi_1 dihedral restraints:     124       0      0  68.060  68.060      37.037       1.000
15 Sidechain Chi_2 dihedral restraints:      94       0      2  78.053  78.053      46.700       1.000
16 Sidechain Chi_3 dihedral restraints:      42       0      1  82.328  82.328      31.651       1.000
17 Sidechain Chi_4 dihedral restraints:      23       0      0  97.542  97.542      16.162       1.000
18 Disulfide distance restraints      :       3       0      0   0.022   0.022     0.24811       1.000
19 Disulfide angle restraints         :       6       0      0   2.102   2.102     0.58517       1.000
20 Disulfide dihedral angle restraints:       3       0      0  29.779  29.779      2.4403       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    1244       0      0   0.417   0.417      25.421       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     139      16     25  31.678  63.832      109.21       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     459       0      0   0.695   0.695      29.468       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: LYS_TRINI.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   16661.7832



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   2164  92D  92D N   CA    731  732  123.73  107.00   16.73    4.81  107.00   16.73    4.81

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   4103  38F  38F CA  C     296  304 -154.45 -180.00   25.55    5.11 -180.00   25.55    5.11

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   3935   9L  10A C   N      78   80   51.08  -68.20  120.46   10.75  -62.50 -166.26   29.20
    1         10A  10A N   CA     80   81  162.14  145.30                  -40.90
    2   3936  10A  11L C   N      83   85 -121.99 -108.50   29.63    1.43  -63.50  170.28   27.26
    2         11L  11L N   CA     85   86  158.88  132.50                  -41.20
    3   3937  11L  12A C   N      91   93  -85.00  -68.20   40.72    3.82  -62.50  150.79   23.71
    3         12A  12A N   CA     93   94  108.20  145.30                  -40.90
    4   3938  12A  13A C   N      96   98 -148.57 -134.00   20.83    0.64  -62.50  179.23   33.97
    4         13A  13A N   CA     98   99  161.89  147.00                  -40.90
    5   3939  13A  14L C   N     101  103 -102.43 -108.50   11.19    0.64  -63.50 -178.87   27.53
    5         14L  14L N   CA    103  104  141.90  132.50                  -41.20
    6   3942  16I  17S C   N     123  125  -70.61  -72.40    4.14    0.30  -64.10  168.99   12.64
    6         17S  17S N   CA    125  126  156.13  152.40                  -35.00
    7   3945  19E  20A C   N     144  146 -173.53 -134.00   40.40    1.66  -62.50 -148.86   31.66
    7         20A  20A N   CA    146  147  138.69  147.00                  -40.90
    8   3946  20A  21K C   N     149  151 -175.90 -118.00   57.96    2.14  -62.90 -149.58   34.04
    8         21K  21K N   CA    151  152  141.70  139.10                  -40.80
    9   3947  21K  22Y C   N     158  160 -129.49 -124.30   22.38    1.41  -63.50  170.33   24.12
    9         22Y  22Y N   CA    160  161  113.63  135.40                  -43.40
   10   3948  22Y  23F C   N     170  172 -136.65 -124.20   75.05    3.81  -63.20  135.27   15.28
   10         23F  23F N   CA    172  173   69.29  143.30                  -44.30
   11   3950  24A  25T C   N     186  188  -86.77  -78.10   30.18    1.05  -63.20  141.18   19.68
   11         25T  25T N   CA    188  189  178.71  149.80                  -42.10
   12   3951  25T  26N C   N     193  195  -97.06  -71.20   51.68    2.76  -63.20  135.65   18.89
   12         26N  26N N   CA    195  196 -172.45  142.80                  -41.10
   13   3953  27C  28E C   N     207  209  -71.27  -63.60   49.20    6.99  -63.60   49.20    6.99
   13         28E  28E N   CA    209  210  -88.90  -40.30                  -40.30
   14   4011  85K  86T C   N     689  691   81.27   55.90   51.01    2.46 -124.80 -146.29   12.84
   14         86T  86T N   CA    691  692   -4.75   39.50                  143.50
   15   4017  91K  92D C   N     729  731 -137.01  -63.30   80.35   13.69  -63.30   80.35   13.69
   15         92D  92D N   CA    731  732  -71.96  -40.00                  -40.00
   16   4041 115I 116Y C   N     906  908  -51.50  -98.40   49.49    2.61  -63.50  156.47   25.44
   16        116Y 116Y N   CA    908  909  112.60  128.40                  -43.40


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0    6   19   55   72  120  127  152  147  193  186


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      141
Number of all, selected real atoms                :     1135    1135
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    10783   10783
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2395
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        1207.7847





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    1158       0      1   0.008   0.008      22.665       1.000
 2 Bond angle potential               :    1555       1     10   2.468   2.468      186.73       1.000
 3 Stereochemical cosine torsion poten:     730       0     28  48.315  48.315      269.61       1.000
 4 Stereochemical improper torsion pot:     471       0      0   1.496   1.496      21.989       1.000
 5 Soft-sphere overlap restraints     :    2395       0      0   0.003   0.003      2.9229       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    2217       0      4   0.380   0.380      116.96       1.000
10 Distance restraints 2 (N-O)        :    2375       0     15   0.435   0.435      178.40       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     140       1      4   5.378   5.378      47.751       1.000
14 Sidechain Chi_1 dihedral restraints:     124       0      4  75.428  75.428      49.875       1.000
15 Sidechain Chi_2 dihedral restraints:      94       0      1  77.352  77.352      45.785       1.000
16 Sidechain Chi_3 dihedral restraints:      42       0      0  85.939  85.939      29.554       1.000
17 Sidechain Chi_4 dihedral restraints:      23       0      0  74.928  74.928      17.158       1.000
18 Disulfide distance restraints      :       3       0      0   0.022   0.022     0.25617       1.000
19 Disulfide angle restraints         :       6       0      0   3.006   3.006      1.1967       1.000
20 Disulfide dihedral angle restraints:       3       0      0  26.437  26.437      2.0178       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    1244       0      0   0.485   0.485      32.536       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     139      23     28  30.723  73.130      132.90       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     459       0      0   0.869   0.869      49.490       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: LYS_TRINI.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   18093.2266



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   2164  92D  92D N   CA    731  732  124.06  107.00   17.06    4.91  107.00   17.06    4.91

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   4103  38F  38F CA  C     296  304 -156.52 -180.00   23.48    4.69 -180.00   23.48    4.69

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   3935   9L  10A C   N      78   80  140.47 -134.00   85.72    2.62  -62.50 -131.26   45.52
    1         10A  10A N   CA     80   81  152.77  147.00                  -40.90
    2   3937  11L  12A C   N      91   93  158.63 -134.00   71.13    1.67  -62.50 -156.11   40.53
    2         12A  12A N   CA     93   94  169.82  147.00                  -40.90
    3   3938  12A  13A C   N      96   98  -96.85  -68.20   30.02    2.81  -62.50 -179.45   28.11
    3         13A  13A N   CA     98   99  136.35  145.30                  -40.90
    4   3939  13A  14L C   N     101  103 -104.98 -108.50    9.17    0.45  -63.50  170.36   21.65
    4         14L  14L N   CA    103  104  124.03  132.50                  -41.20
    5   3940  14L  15C C   N     109  111   36.73  -69.10  121.54   11.29 -117.90  166.03    6.68
    5         15C  15C N   CA    111  112 -158.44  141.80                  141.10
    6   3942  16I  17S C   N     123  125  -84.38  -72.40   27.81    1.30  -64.10  148.89   12.11
    6         17S  17S N   CA    125  126  177.50  152.40                  -35.00
    7   3945  19E  20A C   N     144  146  -83.60  -68.20   15.54    1.38  -62.50  177.12   30.11
    7         20A  20A N   CA    146  147  143.24  145.30                  -40.90
    8   3946  20A  21K C   N     149  151 -122.62 -118.00    8.40    0.32  -62.90 -176.90   27.34
    8         21K  21K N   CA    151  152  146.12  139.10                  -40.80
    9   3947  21K  22Y C   N     158  160 -100.92  -98.40    8.60    0.89  -63.50 -176.18   31.09
    9         22Y  22Y N   CA    160  161  136.63  128.40                  -43.40
   10   3948  22Y  23F C   N     170  172  -87.48  -71.40   22.81    2.00  -63.20  170.57   22.10
   10         23F  23F N   CA    172  173  124.53  140.70                  -44.30
   11   3949  23F  24A C   N     181  183 -165.31 -134.00   35.05    0.80  -62.50 -172.85   36.12
   11         24A  24A N   CA    183  184  162.73  147.00                  -40.90
   12   3950  24A  25T C   N     186  188  -66.83  -78.10   16.81    0.60  -63.20  179.46   22.78
   12         25T  25T N   CA    188  189  137.32  149.80                  -42.10
   13   3951  25T  26N C   N     193  195 -125.42 -119.90   15.58    0.57  -63.20  178.53   25.86
   13         26N  26N N   CA    195  196  151.57  137.00                  -41.10
   14   3961  35R  36Q C   N     280  282  -62.66  -63.80    1.17    0.20 -121.10 -171.00    7.85
   14         36Q  36Q N   CA    282  283  -40.04  -40.30                  139.70
   15   3962  36Q  37G C   N     289  291  -86.08  -62.40   28.07    4.22   82.20  171.81   12.61
   15         37G  37G N   CA    291  292  -26.13  -41.20                    8.50
   16   3979  53E  54S C   N     433  435 -137.34  -64.10   78.57    8.64  -64.10   78.57    8.64
   16         54S  54S N   CA    435  436   -6.56  -35.00                  -35.00
   17   4011  85K  86T C   N     689  691   77.88   55.90   46.01    2.20 -124.80 -146.45   12.87
   17         86T  86T N   CA    691  692   -0.92   39.50                  143.50
   18   4017  91K  92D C   N     729  731 -136.72  -63.30   79.29   13.50  -63.30   79.29   13.50
   18         92D  92D N   CA    731  732  -69.95  -40.00                  -40.00
   19   4041 115I 116Y C   N     906  908  -48.57  -98.40   52.60    2.78  -63.50  155.67   25.47
   19        116Y 116Y N   CA    908  909  111.55  128.40                  -43.40
   20   4044 118R 119H C   N     938  940  -92.35 -125.60   70.92    2.01  -63.20  121.99   13.68
   20        119H 119H N   CA    940  941   76.15  138.80                  -42.30
   21   4045 119H 120K C   N     948  950  -60.91  -62.90   31.39    3.97 -118.00  159.34    8.23
   21        120K 120K N   CA    950  951  -72.13  -40.80                  139.10
   22   4055 129N 130H C   N    1045 1047 -119.51  -63.20   73.77    8.59  -63.20   73.77    8.59
   22        130H 130H N   CA   1047 1048    5.35  -42.30                  -42.30
   23   4056 130H 131C C   N    1055 1057 -121.66  -63.00   60.52    9.18  -63.00   60.52    9.18
   23        131C 131C N   CA   1057 1058  -26.24  -41.10                  -41.10


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0   10   15   58   61  120  118  136  169  175  188


<< end of ENERGY.

>> Summary of successfully produced models:
Filename                          molpdf
----------------------------------------
LYS_TRINI.B99990001.pdb       1088.79382
LYS_TRINI.B99990002.pdb       1207.78467

In [32]:
#Визуализируем модель 1 
Image("Lysosim.png", width = 700)
Out[32]:
In [33]:
#Визуализируем модель 2
Image("Lysosim2.png", width = 700)
Out[33]:
Видим, что структуры получились довольно похожие, выделяется длинная петля у анализируемой последовательности

Добавим лиганд к новой структуре

In [18]:
seq_liganded = ''
for res in alignm[0].residues:
    seq_liganded += res.code
for lig in alignm[1].residues[-3:]:
    seq_liganded += lig.code
alignm.append_sequence(seq_liganded)
alignm[2].code = 'LYS_TRINI_withlig'
del alignm[0]
In [19]:
# Делаем выравнивание.
alignm.salign()
# Сохраняем в файл.
alignm.write(file='all_in_one2.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration    1
In [20]:
# Смотрим на выравнивание.
! cat all_in_one2.ali
>P1;1lmp
structureX:1lmp.pdb:   1 :A:+132 :A:MOL_ID  1; MOLECULE  LYSOZYME; CHAIN  A; SYNONYM  MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC  3.2.1.17:MOL_ID  1; ORGANISM_SCIENTIFIC  ONCORHYNCHUS MYKISS; ORGANISM_COMMON  RAINBOW TROUT; ORGANISM_TAXID  8022; ORGAN  KIDNEY: 2.00: 0.16
KVYDRCELA------------------RALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNR-NTDGSTDYGIF
QINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV..
.*

>P1;LYS_TRINI_withlig
sequence::1    : :+144 : :undefined:undefined:-1.00:-1.00
MQKLRVFLLALAALCISCEAKYFATNCELVHELRRQGFPEDKMRDWVCLIQNESGRNTSKMGTINKNGSRDYGLF
QINDKYWCSKTSTPGKD--CNVTCAEMLLDDITKASKCAKKI-YKRHKFQAWYGWRNHCQG----TLPDISKC..
.*
In [21]:
# выбираем объект для моделирования 
s = alignm[1]
pdb = alignm[0]

# создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='all_in_one2.ali', knowns=pdb.code, sequence=s.code)

a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
automodel__W> Topology and/or parameter libraries already in memory. These will
                be used instead of the automodel defaults. If this is not what you
                want, clear them before creating the automodel object with
                env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)

check_ali___> Checking the sequence-structure alignment. 

Implied intrachain target CA(i)-CA(i+1) distances longer than  8.0 angstroms:

ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
----------------------------------------------
     92     1   73    76      D     C    8.895
    136     1  117   122      G     T   13.814
END OF TABLE

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:     2   141
              atom names           : C     +N
              atom indices         :  1133     0

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:     2   141
              atom names           : C     CA    +N    O
              atom indices         :  1133  1130     0  1134
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL:        3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
              Default CHARMM atom type assigned:  C1 -->  CT2
              This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:    13130    12126
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      144
Number of all, selected real atoms                :     1178    1178
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    12126   12126
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2686
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        1423.5923





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    1158       0      1   0.009   0.009      28.607       1.000
 2 Bond angle potential               :    1555       2     13   2.533   2.533      198.01       1.000
 3 Stereochemical cosine torsion poten:     730       0     39  49.961  49.961      285.10       1.000
 4 Stereochemical improper torsion pot:     471       0      0   1.645   1.645      26.244       1.000
 5 Soft-sphere overlap restraints     :    2686       1      2   0.008   0.008      21.658       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    2202       0      8   0.519   0.519      190.41       1.000
10 Distance restraints 2 (N-O)        :    2360       0     13   0.549   0.549      211.56       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     140       1      6   5.712   5.712      53.874       1.000
14 Sidechain Chi_1 dihedral restraints:     124       0      5  81.850  81.850      51.516       1.000
15 Sidechain Chi_2 dihedral restraints:      94       0      0  77.914  77.914      41.901       1.000
16 Sidechain Chi_3 dihedral restraints:      42       0      0  78.563  78.563      28.440       1.000
17 Sidechain Chi_4 dihedral restraints:      23       0      0  92.985  92.985      17.043       1.000
18 Disulfide distance restraints      :       3       0      0   0.019   0.019     0.19031       1.000
19 Disulfide angle restraints         :       6       0      0   3.736   3.736      1.8492       1.000
20 Disulfide dihedral angle restraints:       3       0      0  43.872  43.872      4.1162       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    1225       0      0   0.385   0.385      22.829       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     139      24     35  35.659  73.818      176.06       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     462       0      0   0.762   0.762      37.510       1.000
27 Distance restraints 5 (X-Y)        :    1389       0      2   0.048   0.048      26.659       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: LYS_TRINI_withlig.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   19517.2773



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1447  28E  28E N   CA    209  210  126.52  107.00   19.52    5.61  107.00   19.52    5.61
    2   2164  92D  92D N   CA    731  732  124.52  107.00   17.52    5.04  107.00   17.52    5.04

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   4103  38F  38F CA  C     296  304 -156.98 -180.00   23.02    4.60 -180.00   23.02    4.60

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   3935   9L  10A C   N      78   80   63.08  -68.20  131.59   10.85  -62.50 -142.76   42.23
    1         10A  10A N   CA     80   81  136.37  145.30                  -40.90
    2   3936  10A  11L C   N      83   85 -137.65 -108.50   29.34    1.44  -63.50 -174.21   22.86
    2         11L  11L N   CA     85   86  129.15  132.50                  -41.20
    3   3937  11L  12A C   N      91   93  -70.16  -68.20    3.99    0.38  -62.50  177.44   29.46
    3         12A  12A N   CA     93   94  141.83  145.30                  -40.90
    4   3938  12A  13A C   N      96   98 -157.49 -134.00   27.87    0.67  -62.50 -176.40   35.15
    4         13A  13A N   CA     98   99  161.99  147.00                  -40.90
    5   3939  13A  14L C   N     101  103  -85.26  -70.70   22.81    1.43  -63.50  161.11   23.67
    5         14L  14L N   CA    103  104  159.16  141.60                  -41.20
    6   3942  16I  17S C   N     123  125  -73.28  -72.40    3.21    0.22  -64.10  175.92   13.31
    6         17S  17S N   CA    125  126  149.31  152.40                  -35.00
    7   3944  18C  19E C   N     135  137  -58.51  -69.30   11.35    0.73  -63.60  179.34   24.19
    7         19E  19E N   CA    137  138  138.96  142.50                  -40.30
    8   3945  19E  20A C   N     144  146  -65.03  -68.20    6.68    0.44  -62.50  179.70   29.57
    8         20A  20A N   CA    146  147  139.42  145.30                  -40.90
    9   3946  20A  21K C   N     149  151 -123.80 -118.00    5.80    0.22  -62.90 -170.16   22.13
    9         21K  21K N   CA    151  152  139.00  139.10                  -40.80
   10   3948  22Y  23F C   N     170  172 -118.64 -124.20    5.62    0.24  -63.20 -179.70   28.72
   10         23F  23F N   CA    172  173  144.13  143.30                  -44.30
   11   3949  23F  24A C   N     181  183 -171.70 -134.00   37.79    1.16  -62.50 -158.35   38.84
   11         24A  24A N   CA    183  184  149.58  147.00                  -40.90
   12   3950  24A  25T C   N     186  188 -140.24 -124.80   22.81    1.36  -63.20 -174.43   19.89
   12         25T  25T N   CA    188  189  126.71  143.50                  -42.10
   13   3953  27C  28E C   N     207  209  -83.91  -63.60   49.53    7.74  -63.60   49.53    7.74
   13         28E  28E N   CA    209  210  -85.47  -40.30                  -40.30
   14   4011  85K  86T C   N     689  691   76.17   55.90   44.51    2.13 -124.80 -145.71   12.92
   14         86T  86T N   CA    691  692   -0.13   39.50                  143.50
   15   4017  91K  92D C   N     729  731 -146.87  -63.30   90.90   15.49  -63.30   90.90   15.49
   15         92D  92D N   CA    731  732  -75.77  -40.00                  -40.00
   16   4043 117K 118R C   N     927  929  -59.72 -125.20   81.90    2.42  -63.00  132.55   18.13
   16        118R 118R N   CA    929  930   91.41  140.60                  -41.10
   17   4044 118R 119H C   N     938  940  177.19  -63.20  121.42   18.12  -63.20  121.42   18.12
   17        119H 119H N   CA    940  941  -21.45  -42.30                  -42.30
   18   4045 119H 120K C   N     948  950   51.91  -70.20  145.11   12.02 -118.00 -172.32    8.57
   18        120K 120K N   CA    950  951 -141.20  140.40                  139.10
   19   4055 129N 130H C   N    1045 1047 -124.35  -63.20   71.25    8.96  -63.20   71.25    8.96
   19        130H 130H N   CA   1047 1048   -5.73  -42.30                  -42.30
   20   4058 132Q 133G C   N    1070 1072  131.50   78.70   57.45    2.17   82.20  170.07   10.62
   20        133G 133G N   CA   1072 1073  171.27 -166.10                    8.50
   21   4059 133G 134T C   N    1074 1076 -112.94 -124.80   38.21    1.31  -63.20  157.34   17.39
   21        134T 134T N   CA   1076 1077  107.17  143.50                  -42.10
   22   4061 135L 136P C   N    1089 1091  -76.26  -64.50   35.16    3.26  -58.70  145.63   10.67
   22        136P 136P N   CA   1091 1092  114.07  147.20                  -30.50
   23   4062 136P 137D C   N    1096 1098  -77.99  -70.90   60.52    2.64  -63.30  110.57   14.57
   23        137D 137D N   CA   1098 1099 -149.59  150.30                  -40.00
   24   4065 139S 140K C   N    1118 1120   55.58   56.60    5.13    0.30  -62.90  145.48   25.28
   24        140K 140K N   CA   1120 1121   43.63   38.60                  -40.80


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    1   15   21   86  101  153  134  144  180  206  203


<< end of ENERGY.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      144
Number of all, selected real atoms                :     1178    1178
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    12126   12126
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2564
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        1353.4377





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    1158       0      1   0.009   0.009      29.351       1.000
 2 Bond angle potential               :    1555       2     14   2.501   2.501      190.45       1.000
 3 Stereochemical cosine torsion poten:     730       0     30  49.230  49.230      277.39       1.000
 4 Stereochemical improper torsion pot:     471       0      0   1.338   1.338      18.055       1.000
 5 Soft-sphere overlap restraints     :    2564       2      2   0.008   0.008      21.745       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    2202       1      9   0.503   0.503      182.85       1.000
10 Distance restraints 2 (N-O)        :    2360       0     11   0.534   0.534      216.93       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     140       2      5   5.835   5.835      56.212       1.000
14 Sidechain Chi_1 dihedral restraints:     124       0      1  81.029  81.029      41.756       1.000
15 Sidechain Chi_2 dihedral restraints:      94       0      0  68.389  68.389      40.154       1.000
16 Sidechain Chi_3 dihedral restraints:      42       0      0  78.250  78.250      29.326       1.000
17 Sidechain Chi_4 dihedral restraints:      23       0      0  86.360  86.360      15.054       1.000
18 Disulfide distance restraints      :       3       0      0   0.025   0.025     0.31572       1.000
19 Disulfide angle restraints         :       6       0      0   3.273   3.273      1.4193       1.000
20 Disulfide dihedral angle restraints:       3       0      0  28.228  28.228      1.7621       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    1225       0      0   0.439   0.439      27.915       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     139      23     30  32.740  76.348      135.07       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     462       0      0   0.731   0.731      37.322       1.000
27 Distance restraints 5 (X-Y)        :    1389       0      2   0.052   0.052      30.356       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: LYS_TRINI_withlig.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   19216.9336



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   2164  92D  92D N   CA    731  732  123.93  107.00   16.93    4.87  107.00   16.93    4.87
    2   2653 135L 135L N   CA   1083 1084  122.72  107.00   15.72    4.52  107.00   15.72    4.52

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   4103  38F  38F CA  C     296  304 -155.55 -180.00   24.45    4.89 -180.00   24.45    4.89
    2   4199 134T 134T CA  C    1077 1081 -156.90 -180.00   23.10    4.62 -180.00   23.10    4.62

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   3935   9L  10A C   N      78   80  179.81 -134.00   46.23    1.60  -62.50 -149.97   40.65
    1         10A  10A N   CA     80   81  145.14  147.00                  -40.90
    2   3936  10A  11L C   N      83   85 -167.51 -108.50   59.80    2.97  -63.50 -165.81   23.86
    2         11L  11L N   CA     85   86  122.79  132.50                  -41.20
    3   3937  11L  12A C   N      91   93 -166.06 -134.00   36.73    0.85  -62.50 -174.28   35.92
    3         12A  12A N   CA     93   94  164.93  147.00                  -40.90
    4   3938  12A  13A C   N      96   98 -127.56 -134.00    8.13    0.45  -62.50  179.35   32.87
    4         13A  13A N   CA     98   99  151.97  147.00                  -40.90
    5   3939  13A  14L C   N     101  103  -94.10 -108.50   25.79    1.21  -63.50  155.35   20.03
    5         14L  14L N   CA    103  104  111.11  132.50                  -41.20
    6   3942  16I  17S C   N     123  125  -62.63  -72.40   15.89    1.24  -64.10  160.07   11.51
    6         17S  17S N   CA    125  126  164.94  152.40                  -35.00
    7   3944  18C  19E C   N     135  137  -89.38  -69.30   26.87    2.47  -63.60  166.95   20.95
    7         19E  19E N   CA    137  138  124.64  142.50                  -40.30
    8   3947  21K  22Y C   N     158  160 -133.67 -124.30   15.49    0.63  -63.50 -177.13   32.51
    8         22Y  22Y N   CA    160  161  147.73  135.40                  -43.40
    9   3948  22Y  23F C   N     170  172 -125.76 -124.20   10.91    0.55  -63.20 -172.45   22.32
    9         23F  23F N   CA    172  173  132.51  143.30                  -44.30
   10   3949  23F  24A C   N     181  183 -132.70 -134.00   12.36    0.67  -62.50 -170.88   28.51
   10         24A  24A N   CA    183  184  134.71  147.00                  -40.90
   11   3950  24A  25T C   N     186  188 -111.05 -124.80   14.71    0.63  -63.20 -174.10   27.03
   11         25T  25T N   CA    188  189  138.26  143.50                  -42.10
   12   3951  25T  26N C   N     193  195 -123.31 -119.90    7.27    0.39  -63.20 -178.10   20.07
   12         26N  26N N   CA    195  196  130.58  137.00                  -41.10
   13   3989  63T  64I C   N     503  505  -63.43  -63.40   12.87    2.11 -120.60  170.88    7.72
   13         64I  64I N   CA    505  506  -30.73  -43.60                  130.30
   14   4011  85K  86T C   N     689  691   80.54   55.90   48.65    2.35 -124.80 -147.36   12.80
   14         86T  86T N   CA    691  692   -2.45   39.50                  143.50
   15   4017  91K  92D C   N     729  731 -138.24  -63.30   80.63   13.71  -63.30   80.63   13.71
   15         92D  92D N   CA    731  732  -69.75  -40.00                  -40.00
   16   4041 115I 116Y C   N     906  908  -49.64  -98.40   54.98    3.47  -63.50  147.05   24.05
   16        116Y 116Y N   CA    908  909  102.99  128.40                  -43.40
   17   4044 118R 119H C   N     938  940  -86.96 -125.60   53.36    1.32  -63.20  146.24   16.93
   17        119H 119H N   CA    940  941  102.00  138.80                  -42.30
   18   4056 130H 131C C   N    1055 1057  -76.95  -63.00   79.79   10.75  -63.00   79.79   10.75
   18        131C 131C N   CA   1057 1058 -119.66  -41.10                  -41.10
   19   4058 132Q 133G C   N    1070 1072  109.68   78.70   64.24    0.96   82.20  132.01    7.75
   19        133G 133G N   CA   1072 1073  137.62 -166.10                    8.50
   20   4059 133G 134T C   N    1074 1076  140.13  -63.20  160.17   26.55  -63.20  160.17   26.55
   20        134T 134T N   CA   1076 1077  -75.37  -42.10                  -42.10
   21   4062 136P 137D C   N    1096 1098   36.17  -70.90  122.88   10.31  -63.30  147.86   16.41
   21        137D 137D N   CA   1098 1099 -149.40  150.30                  -40.00
   22   4064 138I 139S C   N    1112 1114 -132.79 -136.60   47.60    2.33  -64.10  154.83    9.84
   22        139S 139S N   CA   1114 1115  103.75  151.20                  -35.00
   23   4065 139S 140K C   N    1118 1120  -57.74  -70.20   28.66    1.80  -62.90  155.47   20.48
   23        140K 140K N   CA   1120 1121  114.58  140.40                  -40.80


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    1   13   16   66   84  132  139  134  174  202  204


<< end of ENERGY.

>> Summary of successfully produced models:
Filename                          molpdf
----------------------------------------
LYS_TRINI_withlig.B99990001.pdb     1423.59229
LYS_TRINI_withlig.B99990002.pdb     1353.43774

In [22]:
#Визуализируем модель 1 с лигандом 
Image("Lysosim_lig.png", width = 700)
Out[22]:
In [23]:
#Визуализируем модель 2 с лигандом 
Image("Lysosim_lig2.png", width = 700)
Out[23]:
Видим, что молекулы лигандов совпали

Передвинем лиганд в другое место

In [36]:
class mymodel(modeller.automodel.automodel):
    def special_restraints(self, aln):
        rsr = self.restraints
        at = self.atoms
        for x,y in [('O:123','CA:114')]:
            rsr.add(modeller.forms.gaussian(group=modeller.physical.xy_distance, 
                                            feature=modeller.features.distance(
                                            at[x],at[y]),mean=3.0, stdev=0.1))

from modeller import *
from modeller.automodel import *    
a = mymodel(env, alnfile='all_in_one2.ali', knowns=pdb.code, sequence=s.code)
automodel__W> Topology and/or parameter libraries already in memory. These will
                be used instead of the automodel defaults. If this is not what you
                want, clear them before creating the automodel object with
                env.libs.topology.clear() and env.libs.parameters.clear()
In [37]:
a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)

check_ali___> Checking the sequence-structure alignment. 

Implied intrachain target CA(i)-CA(i+1) distances longer than  8.0 angstroms:

ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
----------------------------------------------
     92     1   73    76      D     C    8.895
    136     1  117   122      G     T   13.814
END OF TABLE

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:     2   141
              atom names           : C     +N
              atom indices         :  1133     0

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:     2   141
              atom names           : C     CA    +N    O
              atom indices         :  1133  1130     0  1134
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
patch_s_522_> Number of disulfides patched in MODEL:        3
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
              Default CHARMM atom type assigned:  C1 -->  CT2
              This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:    13131    12127


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      144
Number of all, selected real atoms                :     1178    1178
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    12127   12127
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2646
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        1959.1710





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    1158       0      1   0.010   0.010      36.531       1.000
 2 Bond angle potential               :    1555       3     19   2.707   2.707      219.74       1.000
 3 Stereochemical cosine torsion poten:     730       0     43  50.675  50.675      286.04       1.000
 4 Stereochemical improper torsion pot:     471       1      3   1.769   1.769      36.262       1.000
 5 Soft-sphere overlap restraints     :    2646       1      3   0.009   0.009      24.258       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    2202       8     28   0.646   0.646      337.79       1.000
10 Distance restraints 2 (N-O)        :    2360       6     30   0.659   0.659      367.59       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     140       1     10   6.388   6.388      67.362       1.000
14 Sidechain Chi_1 dihedral restraints:     124       0      2  77.924  77.924      49.748       1.000
15 Sidechain Chi_2 dihedral restraints:      94       0      1  73.267  73.267      44.583       1.000
16 Sidechain Chi_3 dihedral restraints:      42       0      0  81.976  81.976      30.666       1.000
17 Sidechain Chi_4 dihedral restraints:      23       0      0  82.889  82.889      14.456       1.000
18 Disulfide distance restraints      :       3       0      0   0.022   0.022     0.25096       1.000
19 Disulfide angle restraints         :       6       0      0   2.276   2.276     0.68613       1.000
20 Disulfide dihedral angle restraints:       3       0      0  18.572  18.572      1.0851       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    1225       0      0   0.451   0.451      34.984       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     139      27     35  39.965  74.508      240.73       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     462       0      2   0.982   0.982      55.439       1.000
27 Distance restraints 5 (X-Y)        :    1390       1      5   0.078   0.078      110.97       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: LYS_TRINI_withlig.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   20360.7461



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   2164  92D  92D N   CA    731  732  124.25  107.00   17.25    4.96  107.00   17.25    4.96
    2   2653 135L 135L N   CA   1083 1084  123.29  107.00   16.29    4.69  107.00   16.29    4.69

-------------------------------------------------------------------------------------------------

Feature  4                           : Stereochemical improper torsion potentia
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   3854 123A 123A C   CA    982  980   13.23    0.00   13.23    4.66    0.00   13.23    4.66

-------------------------------------------------------------------------------------------------

Feature 10                           : Distance restraints 2 (N-O)             
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   8755 122Q 115I N   O     970  907   10.87    7.52    3.35    4.65    7.52    3.35    4.65
    2   8773 123A 115I N   O     979  907   10.12    6.71    3.41    5.82    6.71    3.41    5.82
    3   8796 124W 115I N   O     984  907   10.84    7.90    2.94    5.21    7.90    2.94    5.21
    4   8819 125Y 123A N   O     998  983    5.38    3.62    1.76    4.84    3.62    1.76    4.84

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   3935   9L  10A C   N      78   80 -148.12 -134.00   15.60    0.35  -62.50 -173.69   35.11
    1         10A  10A N   CA     80   81  153.63  147.00                  -40.90
    2   3936  10A  11L C   N      83   85  -68.89  -70.70    1.82    0.16  -63.50  177.46   24.95
    2         11L  11L N   CA     85   86  141.42  141.60                  -41.20
    3   3937  11L  12A C   N      91   93  -95.77  -68.20   40.23    3.96  -62.50  160.39   24.87
    3         12A  12A N   CA     93   94  116.00  145.30                  -40.90
    4   3938  12A  13A C   N      96   98 -134.11 -134.00   10.24    0.58  -62.50  177.00   32.84
    4         13A  13A N   CA     98   99  157.24  147.00                  -40.90
    5   3942  16I  17S C   N     123  125 -130.02 -136.60   18.21    0.76  -64.10 -178.39   11.23
    5         17S  17S N   CA    125  126  134.22  151.20                  -35.00
    6   3945  19E  20A C   N     144  146 -103.24 -134.00   33.05    0.76  -62.50 -179.53   27.87
    6         20A  20A N   CA    146  147  134.91  147.00                  -40.90
    7   3947  21K  22Y C   N     158  160  -37.05  -98.40   64.47    2.98  -63.50  170.44   25.73
    7         22Y  22Y N   CA    160  161  148.22  128.40                  -43.40
    8   3948  22Y  23F C   N     170  172  -58.83  -71.40   20.82    1.85  -63.20  158.47   21.71
    8         23F  23F N   CA    172  173  157.29  140.70                  -44.30
    9   3949  23F  24A C   N     181  183 -135.01 -134.00   23.51    1.31  -62.50  165.37   30.98
    9         24A  24A N   CA    183  184  170.48  147.00                  -40.90
   10   3950  24A  25T C   N     186  188  -70.34  -78.10   23.13    1.25  -63.20  146.48   19.26
   10         25T  25T N   CA    188  189  171.59  149.80                  -42.10
   11   3953  27C  28E C   N     207  209 -101.78  -63.60   39.88    6.74  -63.60   39.88    6.74
   11         28E  28E N   CA    209  210  -51.80  -40.30                  -40.30
   12   3961  35R  36Q C   N     280  282  -58.73  -63.80    6.22    1.13 -121.10 -172.92    7.67
   12         36Q  36Q N   CA    282  283  -36.68  -40.30                  139.70
   13   3962  36Q  37G C   N     289  291  -87.37  -62.40   27.21    4.31   82.20  173.97   12.86
   13         37G  37G N   CA    291  292  -30.37  -41.20                    8.50
   14   3979  53E  54S C   N     433  435 -135.30  -64.10   77.09    8.36  -64.10   77.09    8.36
   14         54S  54S N   CA    435  436   -5.43  -35.00                  -35.00
   15   4011  85K  86T C   N     689  691   76.84   55.90   46.57    2.22 -124.80 -144.89   12.96
   15         86T  86T N   CA    691  692   -2.09   39.50                  143.50
   16   4017  91K  92D C   N     729  731 -142.08  -63.30   84.19   14.30  -63.30   84.19   14.30
   16         92D  92D N   CA    731  732  -69.69  -40.00                  -40.00
   17   4038 112A 113K C   N     880  882  -69.42 -118.00   76.68    2.82  -62.90  120.75   15.34
   17        113K 113K N   CA    882  883   79.78  139.10                  -40.80
   18   4039 113K 114K C   N     889  891   32.05  -62.90  127.23   15.79  -62.90  127.23   15.79
   18        114K 114K N   CA    891  892 -125.49  -40.80                  -40.80
   19   4041 115I 116Y C   N     906  908   87.39 -124.30  156.09   12.80  -63.50 -160.73   37.72
   19        116Y 116Y N   CA    908  909   86.75  135.40                  -43.40
   20   4048 122Q 123A C   N     977  979  -74.01  -62.50   80.31   12.65  -62.50   80.31   12.65
   20        123A 123A N   CA    979  980   38.58  -40.90                  -40.90
   21   4055 129N 130H C   N    1045 1047 -128.15  -63.20   82.05    9.75  -63.20   82.05    9.75
   21        130H 130H N   CA   1047 1048    7.84  -42.30                  -42.30
   22   4056 130H 131C C   N    1055 1057 -103.19  -63.00   86.92    9.02  -63.00   86.92    9.02
   22        131C 131C N   CA   1057 1058   35.98  -41.10                  -41.10
   23   4057 131C 132Q C   N    1061 1063  -70.81  -63.80   15.16    2.59 -121.10  173.98    8.92
   23        132Q 132Q N   CA   1063 1064  -53.75  -40.30                  139.70
   24   4058 132Q 133G C   N    1070 1072   17.53   78.70   61.17    3.09   82.20 -173.59   12.10
   24        133G 133G N   CA   1072 1073 -166.33 -166.10                    8.50
   25   4059 133G 134T C   N    1074 1076 -148.30 -124.80   63.64    3.40  -63.20  152.42   16.11
   25        134T 134T N   CA   1076 1077   84.35  143.50                  -42.10
   26   4062 136P 137D C   N    1096 1098   44.27  -70.90  126.33   10.58  -63.30  159.50   17.72
   26        137D 137D N   CA   1098 1099 -157.77  150.30                  -40.00
   27   4065 139S 140K C   N    1118 1120   58.56   56.60    7.43    0.68  -62.90  149.15   25.91
   27        140K 140K N   CA   1120 1121   45.77   38.60                  -40.80

-------------------------------------------------------------------------------------------------

Feature 27                           : Distance restraints 5 (X-Y)             
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1  12127 123A 114K O   CA    983  892    4.45    3.00    1.45   14.46    3.00    1.45   14.46


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    2   17   22   86   82  135  133  172  171  175  206


<< end of ENERGY.
iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      144
Number of all, selected real atoms                :     1178    1178
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :    12127   12127
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     2740
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        2088.0029





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :    1158       0      1   0.011   0.011      42.199       1.000
 2 Bond angle potential               :    1555       3     21   2.704   2.704      225.53       1.000
 3 Stereochemical cosine torsion poten:     730       0     40  51.338  51.338      297.48       1.000
 4 Stereochemical improper torsion pot:     471       0      2   1.858   1.858      39.909       1.000
 5 Soft-sphere overlap restraints     :    2740       1      2   0.010   0.010      31.486       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    2202       8     26   0.663   0.663      374.49       1.000
10 Distance restraints 2 (N-O)        :    2360       2     31   0.656   0.656      374.58       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     140       6     11   7.820   7.820      100.95       1.000
14 Sidechain Chi_1 dihedral restraints:     124       0      2  77.530  77.530      44.268       1.000
15 Sidechain Chi_2 dihedral restraints:      94       0      2  78.126  78.126      42.676       1.000
16 Sidechain Chi_3 dihedral restraints:      42       0      0  89.166  89.166      32.997       1.000
17 Sidechain Chi_4 dihedral restraints:      23       0      0  95.519  95.519      12.958       1.000
18 Disulfide distance restraints      :       3       0      0   0.021   0.021     0.21848       1.000
19 Disulfide angle restraints         :       6       0      0   2.054   2.054     0.55892       1.000
20 Disulfide dihedral angle restraints:       3       0      0  39.182  39.182      3.0534       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :    1225       0      0   0.481   0.481      38.015       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     139      29     33  38.524  79.112      228.97       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     462       0      0   1.010   1.010      59.121       1.000
27 Distance restraints 5 (X-Y)        :    1390       1      6   0.085   0.085      138.55       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: LYS_TRINI_withlig.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   21648.9297



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  2                           : Bond angle potential                    
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1480  31H  31H N   CA    233  234  123.38  107.00   16.38    4.71  107.00   16.38    4.71
    2   2164  92D  92D N   CA    731  732  126.74  107.00   19.74    5.68  107.00   19.74    5.68
    3   2393 115I 115I N   CA    900  901  123.31  107.00   16.31    4.69  107.00   16.31    4.69

-------------------------------------------------------------------------------------------------

Feature 10                           : Distance restraints 2 (N-O)             
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   8819 125Y 123A N   O     998  983    5.38    3.62    1.76    4.83    3.62    1.76    4.83

-------------------------------------------------------------------------------------------------

Feature 13                           : Mainchain Omega dihedral restraints     
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   4103  38F  38F CA  C     296  304 -152.13 -180.00   27.87    5.57 -180.00   27.87    5.57
    2   4178 113K 113K CA  C     883  889 -154.49 -180.00   25.51    5.10 -180.00   25.51    5.10
    3   4180 115I 115I CA  C     901  906 -150.75 -180.00   29.25    5.85 -180.00   29.25    5.85

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   3935   9L  10A C   N      78   80  -78.72  -68.20   23.90    1.58  -62.50  153.20   25.93
    1         10A  10A N   CA     80   81  166.76  145.30                  -40.90
    2   3936  10A  11L C   N      83   85  -78.20  -70.70   22.63    1.47  -63.50  156.54   22.61
    2         11L  11L N   CA     85   86  162.95  141.60                  -41.20
    3   3937  11L  12A C   N      91   93 -115.16 -134.00   20.80    1.03  -62.50  171.57   30.92
    3         12A  12A N   CA     93   94  155.82  147.00                  -40.90
    4   3938  12A  13A C   N      96   98  -56.30  -68.20   26.69    1.76  -62.50  162.43   26.93
    4         13A  13A N   CA     98   99  121.42  145.30                  -40.90
    5   3939  13A  14L C   N     101  103 -133.34 -108.50   25.13    1.16  -63.50 -169.22   23.58
    5         14L  14L N   CA    103  104  136.34  132.50                  -41.20
    6   3942  16I  17S C   N     123  125 -116.50 -136.60   44.06    1.72  -64.10  156.05    9.62
    6         17S  17S N   CA    125  126  111.99  151.20                  -35.00
    7   3944  18C  19E C   N     135  137 -141.01 -117.80   23.50    0.78  -63.60 -164.82   30.37
    7         19E  19E N   CA    137  138  140.53  136.80                  -40.30
    8   3945  19E  20A C   N     144  146 -128.30 -134.00    7.91    0.46  -62.50  179.14   32.88
    8         20A  20A N   CA    146  147  152.48  147.00                  -40.90
    9   3948  22Y  23F C   N     170  172   84.96 -124.20  150.95    6.06  -63.20 -128.36   26.27
    9         23F  23F N   CA    172  173  137.64  143.30                  -44.30
   10   3949  23F  24A C   N     181  183 -135.74 -134.00   15.83    0.93  -62.50 -172.91   28.15
   10         24A  24A N   CA    183  184  131.26  147.00                  -40.90
   11   3950  24A  25T C   N     186  188 -123.84 -124.80    9.35    0.37  -63.20 -173.56   20.54
   11         25T  25T N   CA    188  189  134.20  143.50                  -42.10
   12   3951  25T  26N C   N     193  195 -124.42 -119.90   28.36    1.18  -63.20  165.63   24.18
   12         26N  26N N   CA    195  196  165.00  137.00                  -41.10
   13   3956  30V  31H C   N     231  233  178.75 -125.60   70.19    3.14  -63.20 -178.14   19.92
   13         31H  31H N   CA    233  234   96.03  138.80                  -42.30
   14   3964  38F  39P C   N     304  306  -19.92  -58.70   44.10    4.11  -64.50  167.36   14.91
   14         39P  39P N   CA    306  307  -51.48  -30.50                  147.20
   15   3965  39P  40E C   N     311  313 -153.77 -117.80  100.62    5.49   54.60  151.63   17.86
   15         40E  40E N   CA    313  314   42.84  136.80                   42.40
   16   3979  53E  54S C   N     433  435 -137.73  -64.10   82.25    8.55  -64.10   82.25    8.55
   16         54S  54S N   CA    435  436    1.65  -35.00                  -35.00
   17   3989  63T  64I C   N     503  505  -63.12  -63.40   13.49    2.22 -120.60  170.41    7.68
   17         64I  64I N   CA    505  506  -30.12  -43.60                  130.30
   18   4011  85K  86T C   N     689  691   75.19   55.90   26.34    1.64 -124.80 -158.82   12.20
   18         86T  86T N   CA    691  692   21.56   39.50                  143.50
   19   4012  86T  87S C   N     696  698 -141.39  -64.10   91.49    8.85  -64.10   91.49    8.85
   19         87S  87S N   CA    698  699   13.95  -35.00                  -35.00
   20   4017  91K  92D C   N     729  731  179.64  -96.50   93.31    3.80  -63.30  162.89   18.52
   20         92D  92D N   CA    731  732   73.28  114.20                  -40.00
   21   4038 112A 113K C   N     880  882  -60.66 -118.00   71.55    2.42  -62.90  137.12   17.93
   21        113K 113K N   CA    882  883   96.30  139.10                  -40.80
   22   4041 115I 116Y C   N     906  908   14.70  -98.40  123.76    7.30  -63.50  144.54   26.61
   22        116Y 116Y N   CA    908  909   78.15  128.40                  -43.40
   23   4048 122Q 123A C   N     977  979  -72.13  -62.50   74.70   11.81  -62.50   74.70   11.81
   23        123A 123A N   CA    979  980   33.18  -40.90                  -40.90
   24   4055 129N 130H C   N    1045 1047 -122.21  -63.20   69.25    8.66  -63.20   69.25    8.66
   24        130H 130H N   CA   1047 1048   -6.06  -42.30                  -42.30
   25   4058 132Q 133G C   N    1070 1072  131.14   78.70   56.86    2.17   82.20  170.58   10.63
   25        133G 133G N   CA   1072 1073  171.92 -166.10                    8.50
   26   4059 133G 134T C   N    1074 1076 -113.17 -124.80   33.59    1.13  -63.20  161.98   17.96
   26        134T 134T N   CA   1076 1077  111.98  143.50                  -42.10
   27   4061 135L 136P C   N    1089 1091  -78.83  -64.50   33.36    3.25  -58.70  148.94   10.76
   27        136P 136P N   CA   1091 1092  117.08  147.20                  -30.50
   28   4062 136P 137D C   N    1096 1098  -78.93  -70.90   60.64    2.60  -63.30  110.71   14.65
   28        137D 137D N   CA   1098 1099 -149.60  150.30                  -40.00
   29   4065 139S 140K C   N    1118 1120   57.87   56.60    2.62    0.28  -62.90  145.81   25.38
   29        140K 140K N   CA   1120 1121   40.89   38.60                  -40.80

-------------------------------------------------------------------------------------------------

Feature 27                           : Distance restraints 5 (X-Y)             
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1  12127 123A 114K O   CA    983  892    4.65    3.00    1.65   16.54    3.00    1.65   16.54


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    1   13   29   95   79  144  156  162  192  191  201


<< end of ENERGY.

>> Summary of successfully produced models:
Filename                          molpdf
----------------------------------------
LYS_TRINI_withlig.B99990001.pdb     1959.17102
LYS_TRINI_withlig.B99990002.pdb     2088.00293

In [42]:
Image("Lysosim_moved1.png", width = 700)
Out[42]:
In [43]:
Image("Lysosim_moved.png", width = 700)
Out[43]:
Видно, по коричневым и бирюзовым шарикам, что положение лиганда сместилось, хотя и не сильно.

Заменим все аминокислоты на Ala

In [45]:
alignm = modeller.alignment(env)

mdl = modeller.model(env, file='1lmp.pdb', model_segment=('FIRST:'+'A', 'LAST:'+'A'))
alignm.append_model(mdl, atom_files='1lmp.pdb', align_codes='1lmp')

ala_prot = 'A' * 120 + '...'
alignm.append_sequence(ala_prot)
alignm[0].code = 'pdb'
alignm[1].code = 'ala_changed'
In [46]:
alignm.salign()
alignm.write(file='align_ala.ali', alignment_format='PIR')
SALIGN_____> adding the next group to the alignment; iteration    1
In [47]:
! cat align_ala.ali
>P1;pdb
structureX:1lmp.pdb:   1 :A:+132 :A:MOL_ID  1; MOLECULE  LYSOZYME; CHAIN  A; SYNONYM  MUCOPEPTIDE N-ACETYLMURAMYLHYDROLASE; EC  3.2.1.17:MOL_ID  1; ORGANISM_SCIENTIFIC  ONCORHYNCHUS MYKISS; ORGANISM_COMMON  RAINBOW TROUT; ORGANISM_TAXID  8022; ORGAN  KIDNEY: 2.00: 0.16
KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNV
CGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV...*

>P1;ala_changed
sequence::1    : :+123 : :undefined:undefined:-1.00:-1.00
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA---------AAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA...*
In [48]:
## Выбираем объект для моделирования 
s = alignm[1]
pdb = alignm[0]

print(s.code, pdb.code)

## Создаем объект automodel
a = modeller.automodel.automodel(env, alnfile='align_ala.ali', knowns=pdb.code, sequence=s.code)

a.name = 'mod' + s.code
a.starting_model = 1
a.ending_model = 2
a.make()
ala_changed pdb
automodel__W> Topology and/or parameter libraries already in memory. These will
                be used instead of the automodel defaults. If this is not what you
                want, clear them before creating the automodel object with
                env.libs.topology.clear() and env.libs.parameters.clear()
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)

check_ali___> Checking the sequence-structure alignment. 

Implied intrachain target CA(i)-CA(i+1) distances longer than  8.0 angstroms:

ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
----------------------------------------------
     55     1   55    65      A     A   16.730
END OF TABLE

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:     1   120
              atom names           : C     +N
              atom indices         :   599     0

getf_______W> RTF restraint not found in the atoms list:
              residue type, indices:     1   120
              atom names           : C     CA    +N    O
              atom indices         :   599   597     0   600
fndatmi_285W> Only      129 residues out of      132 contain atoms of type  CA
              (This is usually caused by non-standard residues, such
              as ligands, or by PDB files with missing atoms.)
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
              least one known structure available. MDT, not library, potential is used.
iup2crm_280W> No topology library in memory or assigning a BLK residue.
              Default CHARMM atom type assigned:  C1 -->  CT2
              This message is written only for the first such atom.
43 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
43 atoms in residues without defined topology
constrained to be rigid bodies
condens_443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:     8748     8155


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      123
Number of all, selected real atoms                :      644     644
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     8155    8155
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     1131
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        1149.6335





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     600       0      1   0.008   0.008      12.594       1.000
 2 Bond angle potential               :     839       0      5   2.294   2.294      91.242       1.000
 3 Stereochemical cosine torsion poten:     244       0     30  74.546  74.546      221.70       1.000
 4 Stereochemical improper torsion pot:     240       0      0   0.986   0.986      6.0719       1.000
 5 Soft-sphere overlap restraints     :    1131       1      2   0.011   0.011      16.749       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    1968       8     30   0.807   0.807      289.51       1.000
10 Distance restraints 2 (N-O)        :    2093       7     34   0.779   0.779      392.30       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     119       0      5   5.513   5.513      42.649       1.000
14 Sidechain Chi_1 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
15 Sidechain Chi_2 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
16 Sidechain Chi_3 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
17 Sidechain Chi_4 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :     668       0      0   0.283   0.283      5.9001       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     118      18     17  31.178  65.702      51.578       1.000
26 Distance restraints 4 (SDCH-SDCH)  :      50       0      1   1.007   1.007      4.0650       1.000
27 Distance restraints 5 (X-Y)        :    1216       0      0   0.037   0.037      15.270       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: ala_changed.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   11512.1084



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  9                           : Distance restraints 1 (CA-CA)           
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   3583  56A  63A CA  CA    277  312   13.26    7.04    6.22    5.87    7.04    6.22    5.87
    2   3584  56A  64A CA  CA    277  317   13.71    7.69    6.02    4.69    7.69    6.02    4.69
    3   3585  56A  65A CA  CA    277  322   10.91    5.45    5.47    6.29    5.45    5.47    6.29
    4   3588  56A  68A CA  CA    277  337   12.20    7.46    4.74    4.60    7.46    4.74    4.60
    5   3589  56A  69A CA  CA    277  342   10.10    6.07    4.03    5.66    6.07    4.03    5.66
    6   3590  56A  70A CA  CA    277  347    9.93    4.69    5.24    7.48    4.69    5.24    7.48

-------------------------------------------------------------------------------------------------

Feature 10                           : Distance restraints 2 (N-O)             
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   4905  38A  55A N   O     186  275    8.42    5.51    2.91    4.97    5.51    2.91    4.97
    2   5216  56A  63A N   O     276  315   13.95    7.89    6.07    4.92    7.89    6.07    4.92
    3   5217  56A  64A N   O     276  320   13.15    7.21    5.93    4.51    7.21    5.93    4.51
    4   5218  56A  65A N   O     276  325   13.40    6.37    7.03    6.65    6.37    7.03    6.65
    5   5221  56A  68A N   O     276  340   12.57    7.02    5.55    5.18    7.02    5.55    5.18
    6   5222  56A  69A N   O     276  345    8.95    2.70    6.25   12.21    2.70    6.25   12.21
    7   5389  71A  56A N   O     351  280    6.09    2.97    3.11    6.58    2.97    3.11    6.58

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1938  15A  16A C   N      74   76   79.55   55.40   27.79    2.07  -62.50  156.37   31.76
    1         16A  16A N   CA     76   77   24.46   38.20                  -40.90
    2   1941  18A  19A C   N      89   91   64.96   55.40   18.81    0.71  -62.50  142.13   28.89
    2         19A  19A N   CA     91   92   22.00   38.20                  -40.90
    3   1943  20A  21A C   N      99  101   61.99  -68.20  146.26   14.16  -62.50  164.25   25.83
    3         21A  21A N   CA    101  102 -148.04  145.30                  -40.90
    4   1944  21A  22A C   N     104  106 -108.73 -134.00   87.19    4.23  -62.50  114.22   17.17
    4         22A  22A N   CA    106  107   63.55  147.00                  -40.90
    5   1945  22A  23A C   N     109  111  -71.36  -62.50   10.50    2.13 -134.00  177.86   10.95
    5         23A  23A N   CA    111  112  -46.53  -40.90                  147.00
    6   1959  36A  37A C   N     179  181   66.14   55.40   13.59    0.85  -62.50  146.82   29.86
    6         37A  37A N   CA    181  182   29.87   38.20                  -40.90
    7   1960  37A  38A C   N     184  186   60.60   55.40    8.45    0.37  -62.50  142.83   29.04
    7         38A  38A N   CA    186  187   31.54   38.20                  -40.90
    8   1971  48A  49A C   N     239  241   83.70   55.40   37.50    2.18  -62.50  156.02   31.57
    8         49A  49A N   CA    241  242   13.59   38.20                  -40.90
    9   1980  57A  58A C   N     284  286   56.09   55.40    8.55    0.57  -62.50  147.45   29.87
    9         58A  58A N   CA    286  287   46.72   38.20                  -40.90
   10   1984  61A  62A C   N     304  306   57.67   55.40    6.13    0.23  -62.50  140.82   28.63
   10         62A  62A N   CA    306  307   32.50   38.20                  -40.90
   11   1986  63A  64A C   N     314  316  -77.90  -68.20   10.90    0.75  -62.50  169.54   28.57
   11         64A  64A N   CA    316  317  150.26  145.30                  -40.90
   12   1987  64A  65A C   N     319  321  -85.37  -68.20   37.84    3.58  -62.50  154.19   24.25
   12         65A  65A N   CA    321  322  111.58  145.30                  -40.90
   13   1989  66A  67A C   N     329  331  -94.83  -68.20   51.08    4.91  -62.50  146.24   22.61
   13         67A  67A N   CA    331  332  101.72  145.30                  -40.90
   14   1990  67A  68A C   N     334  336  -60.72  -68.20   39.47    2.92  -62.50  147.46   24.25
   14         68A  68A N   CA    336  337  106.55  145.30                  -40.90
   15   2017  94A  95A C   N     469  471   79.52 -134.00  160.77    3.65  -62.50  177.12   28.38
   15         95A  95A N   CA    471  472 -146.73  147.00                  -40.90
   16   2030 107A 108A C   N     534  536   53.77   55.40    2.67    0.12  -62.50  141.82   28.77
   16        108A 108A N   CA    536  537   40.32   38.20                  -40.90
   17   2039 116A 117A C   N     579  581   66.39   55.40   36.39    1.42  -62.50  136.32   27.54
   17        117A 117A N   CA    581  582    3.51   38.20                  -40.90
   18   2041 118A 119A C   N     589  591  133.04 -134.00  131.18    3.94  -62.50 -177.30   37.13
   18        119A 119A N   CA    591  592 -120.45  147.00                  -40.90


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0    4    4   37   48   66   53   82   95  102   64


<< end of ENERGY.


>> ENERGY; Differences between the model's features and restraints:
Number of all residues in MODEL                   :      123
Number of all, selected real atoms                :      644     644
Number of all, selected pseudo atoms              :        0       0
Number of all static, selected restraints         :     8155    8155
COVALENT_CYS                                      :        F
NONBONDED_SEL_ATOMS                               :        1
Number of non-bonded pairs (excluding 1-2,1-3,1-4):     1129
Dynamic pairs routine                             : 2, NATM x NATM cell sorting
Atomic shift for contacts update (UPDATE_DYNAMIC) :    0.390
LENNARD_JONES_SWITCH                              :    6.500   7.500
COULOMB_JONES_SWITCH                              :    6.500   7.500
RESIDUE_SPAN_RANGE                                :        0   99999
NLOGN_USE                                         :       15
CONTACT_SHELL                                     :    4.000
DYNAMIC_PAIRS,_SPHERE,_COULOMB,_LENNARD,_MODELLER :        T       T       F       F       F
SPHERE_STDV                                       :    0.050
RADII_FACTOR                                      :    0.820
Current energy                                    :        1163.4586





Summary of the restraint violations: 

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     600       0      1   0.008   0.008      11.742       1.000
 2 Bond angle potential               :     839       0      4   2.217   2.217      85.320       1.000
 3 Stereochemical cosine torsion poten:     244       0     33  76.196  76.196      232.32       1.000
 4 Stereochemical improper torsion pot:     240       0      0   0.920   0.920      5.0349       1.000
 5 Soft-sphere overlap restraints     :    1129       1      2   0.011   0.011      15.941       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :    1968       7     25   0.796   0.796      290.74       1.000
10 Distance restraints 2 (N-O)        :    2093       8     34   0.769   0.769      337.75       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:     119       0      3   4.891   4.891      33.575       1.000
14 Sidechain Chi_1 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
15 Sidechain Chi_2 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
16 Sidechain Chi_3 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
17 Sidechain Chi_4 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :     668       0      0   0.390   0.390      11.102       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:     118      25     19  41.468  77.990      110.87       1.000
26 Distance restraints 4 (SDCH-SDCH)  :      50       0      1   1.380   1.380      7.0948       1.000
27 Distance restraints 5 (X-Y)        :    1216       0      0   0.046   0.046      21.968       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000
34 Absolute position restraints       :       0       0      0   0.000   0.000      0.0000       1.000
35 Dihedral angle difference restraint:       0       0      0   0.000   0.000      0.0000       1.000
36 GBSA implicit solvent potential    :       0       0      0   0.000   0.000      0.0000       1.000
37 EM density fitting potential       :       0       0      0   0.000   0.000      0.0000       1.000
38 SAXS restraints                    :       0       0      0   0.000   0.000      0.0000       1.000
39 Symmetry restraints                :       0       0      0   0.000   0.000      0.0000       1.000



# Heavy relative violation of each residue is written to: ala_changed.V99990002
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1
# The sum of all numbers in the file:   12193.0361



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature  9                           : Distance restraints 1 (CA-CA)           
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   3583  56A  63A CA  CA    277  312   12.36    7.04    5.31    5.02    7.04    5.31    5.02
    2   3584  56A  64A CA  CA    277  317   13.94    7.69    6.25    4.87    7.69    6.25    4.87
    3   3585  56A  65A CA  CA    277  322   11.74    5.45    6.29    7.23    5.45    6.29    7.23
    4   3588  56A  68A CA  CA    277  337   12.27    7.46    4.81    4.67    7.46    4.81    4.67
    5   3589  56A  69A CA  CA    277  342    9.90    6.07    3.82    5.37    6.07    3.82    5.37
    6   3590  56A  70A CA  CA    277  347    8.84    4.69    4.15    5.92    4.69    4.15    5.92

-------------------------------------------------------------------------------------------------

Feature 10                           : Distance restraints 2 (N-O)             
List of the RVIOL violations larger than   :       4.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   4905  38A  55A N   O     186  275    8.23    5.51    2.73    4.65    5.51    2.73    4.65
    2   5216  56A  63A N   O     276  315   13.86    7.89    5.97    4.85    7.89    5.97    4.85
    3   5218  56A  65A N   O     276  325   11.23    6.37    4.86    4.59    6.37    4.86    4.59
    4   5220  56A  67A N   O     276  335   12.43    7.89    4.53    4.51    7.89    4.53    4.51
    5   5221  56A  68A N   O     276  340   12.92    7.02    5.89    5.50    7.02    5.89    5.50
    6   5222  56A  69A N   O     276  345    8.34    2.70    5.64   11.02    2.70    5.64   11.02
    7   5389  71A  56A N   O     351  280    5.75    2.97    2.78    5.87    2.97    2.78    5.87
    8   5427  73A  70A N   O     361  350    6.04    3.17    2.86    4.65    3.17    2.86    4.65

-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints     
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1925   2A   3A C   N       9   11  -63.15  -62.50    9.77    1.63  -68.20  164.13   13.42
    1          3A   3A N   CA     11   12  -50.65  -40.90                  145.30
    2   1926   3A   4A C   N      14   16   24.70  -68.20  102.96    7.15  -68.20  102.96    7.15
    2          4A   4A N   CA     16   17  100.91  145.30                  145.30
    3   1938  15A  16A C   N      74   76   78.10   55.40   25.92    1.96  -62.50  155.56   31.61
    3         16A  16A N   CA     76   77   25.68   38.20                  -40.90
    4   1941  18A  19A C   N      89   91   64.57   55.40   20.47    0.74  -62.50  140.86   28.63
    4         19A  19A N   CA     91   92   19.89   38.20                  -40.90
    5   1943  20A  21A C   N      99  101   53.81   55.40    4.19    0.38  -62.50  138.51   28.14
    5         21A  21A N   CA    101  102   34.33   38.20                  -40.90
    6   1944  21A  22A C   N     104  106   62.95   55.40   10.71    0.56  -62.50  144.39   29.37
    6         22A  22A N   CA    106  107   30.60   38.20                  -40.90
    7   1959  36A  37A C   N     179  181   66.20   55.40   14.95    0.81  -62.50  145.91   29.67
    7         37A  37A N   CA    181  182   27.86   38.20                  -40.90
    8   1960  37A  38A C   N     184  186   55.70   55.40    1.33    0.10  -62.50  142.95   29.02
    8         38A  38A N   CA    186  187   39.50   38.20                  -40.90
    9   1971  48A  49A C   N     239  241  154.76 -134.00   73.14    1.87  -62.50 -148.88   41.93
    9         49A  49A N   CA    241  242  163.55  147.00                  -40.90
   10   1972  49A  50A C   N     244  246   90.05 -134.00  136.20    4.21  -68.20  158.55   13.77
   10         50A  50A N   CA    246  247  155.19  147.00                  145.30
   11   1976  53A  54A C   N     264  266   58.16  -68.20  144.29   14.03  -62.50  159.39   25.06
   11         54A  54A N   CA    266  267 -145.04  145.30                  -40.90
   12   1979  56A  57A C   N     279  281 -160.68 -134.00   28.40    1.32  -62.50 -156.57   30.47
   12         57A  57A N   CA    281  282  137.27  147.00                  -40.90
   13   1980  57A  58A C   N     284  286  -66.00  -68.20    5.56    0.37  -62.50  178.94   29.50
   13         58A  58A N   CA    286  287  140.20  145.30                  -40.90
   14   1983  60A  61A C   N     299  301  -64.51  -62.50    2.97    0.59  -68.20  171.66   13.98
   14         61A  61A N   CA    301  302  -43.08  -40.90                  145.30
   15   1986  63A  64A C   N     314  316  -66.45  -68.20    7.11    0.63  -62.50  166.96   27.56
   15         64A  64A N   CA    316  317  152.19  145.30                  -40.90
   16   1988  65A  66A C   N     324  326   78.44  -62.50  148.77   26.22  -62.50  148.77   26.22
   16         66A  66A N   CA    326  327  -88.52  -40.90                  -40.90
   17   1990  67A  68A C   N     334  336   77.41   55.40   31.74    1.63  -62.50  150.78   30.56
   17         68A  68A N   CA    336  337   15.33   38.20                  -40.90
   18   1992  69A  70A C   N     344  346  -66.93  -62.50   20.03    3.52 -134.00  166.66   10.28
   18         70A  70A N   CA    346  347  -60.43  -40.90                  147.00
   19   1993  70A  71A C   N     349  351 -168.27  -62.50  105.96   20.10  -62.50  105.96   20.10
   19         71A  71A N   CA    351  352  -34.66  -40.90                  -40.90
   20   2017  94A  95A C   N     469  471   80.49 -134.00  159.80    3.63  -62.50  178.02   28.54
   20         95A  95A N   CA    471  472 -146.94  147.00                  -40.90
   21   2030 107A 108A C   N     534  536  106.01 -134.00  157.40    4.31  -62.50 -177.44   31.50
   21        108A 108A N   CA    536  537 -111.14  147.00                  -40.90
   22   2031 108A 109A C   N     539  541 -159.63 -134.00   64.82    2.89  -68.20  110.04    7.23
   22        109A 109A N   CA    541  542 -153.47  147.00                  145.30
   23   2038 115A 116A C   N     574  576   58.77  -68.20  134.11   12.63  -68.20  134.11   12.63
   23        116A 116A N   CA    576  577 -171.52  145.30                  145.30
   24   2039 116A 117A C   N     579  581  -81.63  -68.20   72.72    6.33  -62.50  116.31   18.22
   24        117A 117A N   CA    581  582   73.83  145.30                  -40.90
   25   2041 118A 119A C   N     589  591   65.72   55.40   13.90    0.79  -62.50  145.97   29.69
   25        119A 119A N   CA    591  592   28.89   38.20                  -40.90


report______> Distribution of short non-bonded contacts:


DISTANCE1:  0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40
DISTANCE2:  2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50
FREQUENCY:     0    0    0    0    0    3    6   38   52   65   68   75   97   96   77


<< end of ENERGY.

>> Summary of successfully produced models:
Filename                          molpdf
----------------------------------------
ala_changed.B99990001.pdb     1149.63354
ala_changed.B99990002.pdb     1163.45862

In [51]:
#Визуализируем аланины 1
Image("Ala1.png", width = 700)
Out[51]:
In [52]:
#Визуализируем аланины 2
Image("Ala2.png", width = 700)
Out[52]:
Видим, что структура в этом случае не особо поменялась, а строго говоря, даже стала более похожа